The cavefish Triptophysa xiangxiensis is a species of loach belonging to family Cobitidae, order Cypriniformes. It is endemic to longshan county of western Hunan Province of China. In this study,A total of 103 individuals from three T. xiangxiensis populations which obtained from three caves in wulongshan mountain were studied using 16 pairs of microsatellite markers. Using polymorphism information content (PIC), mean heterozygosity (H), number of effective alleles and F-statistics, the genetic diversity and genetic differentiation were evaluated. A total of 83 different alleles were detected in all examined loci．The number of alleles ranged from 3 to 8,with an average number of about 5 per locus．The observed ( HO) and expected heterozygosity( HE) ranged from 0.3625 to 0.9465 and from 0.5386 to 0.9065,respectively．The polymorphism information content for these three populations were 0.2632、0.2313、0.3035. All of which revealed that the genetic diversity in these three T. xiangxiensis populations were low．The analysis of molecular variance( AMOVA) indicated that almost majority of the variance in the T. xiangxiensis was within stocks(92.84%),and 7.16% was among stocks．The result of AMOVA 、F-statistics, Nei’s genetic distance and genetic identity indicated that genetic difference was relatively small and genetic differentiation was low,with high genetic identity between all two populations．The information generated in this study will contribute to the conservation of this endangered T. xiangxiensis species.